Planctomycetes are a phylum of aquatic bacteria and are found in samples of brackish, and marine and freshwater. They reproduce by budding. In structure, the organisms of this group are ovoid and have a holdfast, at the tip of a thin cylindrical extension from the cell body called the stalk, at the nonreproductive end that helps them to attach to each other during budding.

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For a long time bacteria belonging to this group were considered to lack peptidoglycan, (also called murein) in their cell walls, which is an important heteropolymer present in most bacterial cell walls that serves as a protective component. It was thought that instead their walls were made up of glycoprotein which is rich in glutamate. Recently, however, representatives of all three clades within the Planctomycetes were found to possess peptidoglycan-containing cell walls.[1][2]

Planctomycetes have a distinctive morphology with the appearance of membrane-bound internal compartments, often referred to as the paryphoplasm (ribosome-free space), pirellulosome (ribosome-containing space) and nucleoid (condensed nucleic acid region, in these species surrounded by a double membrane).[3][4] Until the discovery of the Poribacteria, planctomycetes were the only bacteria known with these apparent internal compartments.[5] Three-dimensional electron tomography reconstruction of a representative species, Gemmata obscuriglobus, has yielded varying interpretations of this observation. One 2013 study found the appearance of internal compartments to be due to a densely invaginated but continuous single membrane, concluding that only the two compartments typical of Gram-negative bacteria - the cytoplasm and periplasm - are present. However, the excess membrane triples the surface area of the cell relative to its volume, which may be related to Gemmata'ssterol biosynthesis abilities.[6] A 2014 study using similar methods reported confirmation of the earlier enclosed compartment hypothesis.[7]

It has recently been shown that Gemmata obscuriglobus is able to take in large molecules via a process which in some ways resembles endocytosis, the process used by eukaryotic cells to engulf external items.[8][9]

Although the Planctomycetes are renowned for their unusual cellular characteristics, their distinctness from all other bacteria is additionally supported by the shared presence of two conserved signature indels (CSIs).[10] These CSIs demarcate the group from neighboring phyla within the PVC group.[11] An additional CSI has been found that is shared by all Planctomycetes species, with the exception of Kuenenia stuttgartiensis, which is in line with the observation that K. stuttgartiensis forms a deep branch within the phylum.

A conserved signature indel has also been found to be shared by the entire PVC group, including Planctomycetes.[10][11] Planctomycetes also harbours an important conserved signature protein that has been characterized to play an important housekeeping function that is exclusive to members belonging to the PVC clade.[12]

The life cycle of many planctomycetes involves alternation between sessile cells and flagellated swarmer cells. The sessile cells bud to form the flagellated swarmer cells which swim for a while before settling down to attach and begin reproduction.

1.
Taxonomy (biology)
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Taxonomy is the science of defining groups of biological organisms on the basis of shared characteristics and giving names to those groups. The exact definition of taxonomy varies from source to source, but the core of the remains, the conception, naming. There is some disagreement as to whether biological nomenclature is considered a part of taxonomy, the broadest meaning of taxonomy is used here. The word taxonomy was introduced in 1813 by Candolle, in his Théorie élémentaire de la botanique, the term alpha taxonomy is primarily used today to refer to the discipline of finding, describing, and naming taxa, particularly species. In earlier literature, the term had a different meaning, referring to morphological taxonomy, ideals can, it may be said, never be completely realized. They have, however, a value of acting as permanent stimulants. Some of us please ourselves by thinking we are now groping in a beta taxonomy, turrill thus explicitly excludes from alpha taxonomy various areas of study that he includes within taxonomy as a whole, such as ecology, physiology, genetics, and cytology. He further excludes phylogenetic reconstruction from alpha taxonomy, thus, Ernst Mayr in 1968 defined beta taxonomy as the classification of ranks higher than species. This activity is what the term denotes, it is also referred to as beta taxonomy. How species should be defined in a group of organisms gives rise to practical and theoretical problems that are referred to as the species problem. The scientific work of deciding how to define species has been called microtaxonomy, by extension, macrotaxonomy is the study of groups at higher taxonomic ranks, from subgenus and above only, than species. While some descriptions of taxonomic history attempt to date taxonomy to ancient civilizations, earlier works were primarily descriptive, and focused on plants that were useful in agriculture or medicine. There are a number of stages in scientific thinking. Early taxonomy was based on criteria, the so-called artificial systems. Later came systems based on a complete consideration of the characteristics of taxa, referred to as natural systems, such as those of de Jussieu, de Candolle and Bentham. The publication of Charles Darwins Origin of Species led to new ways of thinking about classification based on evolutionary relationships and this was the concept of phyletic systems, from 1883 onwards. This approach was typified by those of Eichler and Engler, the advent of molecular genetics and statistical methodology allowed the creation of the modern era of phylogenetic systems based on cladistics, rather than morphology alone. Taxonomy has been called the worlds oldest profession, and naming and classifying our surroundings has likely been taking place as long as mankind has been able to communicate

2.
Bacteria
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Bacteria constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a number of shapes, ranging from spheres to rods, Bacteria were among the first life forms to appear on Earth, and are present in most of its habitats. Bacteria inhabit soil, water, acidic hot springs, radioactive waste, Bacteria also live in symbiotic and parasitic relationships with plants and animals. Most bacteria have not been characterised, and only half of the bacterial phyla have species that can be grown in the laboratory. The study of bacteria is known as bacteriology, a branch of microbiology, There are typically 40 million bacterial cells in a gram of soil and a million bacterial cells in a millilitre of fresh water. There are approximately 5×1030 bacteria on Earth, forming a biomass which exceeds that of all plants, Bacteria are vital in many stages of the nutrient cycle by recycling nutrients such as the fixation of nitrogen from the atmosphere. The nutrient cycle includes the decomposition of bodies and bacteria are responsible for the putrefaction stage in this process. In March 2013, data reported by researchers in October 2012, was published and it was suggested that bacteria thrive in the Mariana Trench, which with a depth of up to 11 kilometres is the deepest known part of the oceans. Other researchers reported related studies that microbes thrive inside rocks up to 580 metres below the sea floor under 2.6 kilometres of ocean off the coast of the northwestern United States. According to one of the researchers, You can find microbes everywhere—theyre extremely adaptable to conditions, the vast majority of the bacteria in the body are rendered harmless by the protective effects of the immune system, though many are beneficial particularly in the gut flora. However several species of bacteria are pathogenic and cause diseases, including cholera, syphilis, anthrax, leprosy. The most common fatal diseases are respiratory infections, with tuberculosis alone killing about 2 million people per year. In developed countries, antibiotics are used to treat infections and are also used in farming, making antibiotic resistance a growing problem. Once regarded as constituting the class Schizomycetes, bacteria are now classified as prokaryotes. Unlike cells of animals and other eukaryotes, bacterial cells do not contain a nucleus and these evolutionary domains are called Bacteria and Archaea. The ancestors of modern bacteria were unicellular microorganisms that were the first forms of life to appear on Earth, for about 3 billion years, most organisms were microscopic, and bacteria and archaea were the dominant forms of life. In 2008, fossils of macroorganisms were discovered and named as the Francevillian biota, however, gene sequences can be used to reconstruct the bacterial phylogeny, and these studies indicate that bacteria diverged first from the archaeal/eukaryotic lineage. Bacteria were also involved in the second great evolutionary divergence, that of the archaea, here, eukaryotes resulted from the entering of ancient bacteria into endosymbiotic associations with the ancestors of eukaryotic cells, which were themselves possibly related to the Archaea

3.
Planctobacteria
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Planctobacteria is a taxon created by Cavalier-Smith, specifically a division. However, it is not followed by the scientific community. Cavalier-Smith postulated that the Planctobacteria probably lost or reduced their peptidoglycan cell wall twice, in the Cavalier-Smith bacterial megaclassification, it is within the bacterial Gracilicutes infrakingdom and comprises the phyla Chlamydiae, Lentisphaerae, Planctomycetes, Verrucomicrobia. It has been hypothesised that a member of the PVC clade might have been the host cell in the event that gave rise to the first proto-eukaryotic cell. An important molecular marker in the form of a conserved signature protein has found to be consistently shared by PVC members. The conserved signature protein may be a marker that represents a synapomorphic quality, recent studies have characterized this protein and it has been attributed to play an important housekeeping function in DNA/RNA binding. This observation not only provides a means to demarcate the PVC superphylum, conserved signature indels have also been found specific for the Planctomycetes, Verrucomicrobia, and Chlamydiae that distinguish each respective phylum from one another, and from other bacteria. A three-amino-acid insert in the RNA polymerase protein RpoB has been found that is shared by all sequenced Verrucomicrobia, Chlamydiae, the CSI is absent from neighbouring Planctomycetes and Poribacteria, suggesting common ancestry among the groups for which the CSI is specific. Additional lines of evidence for the existence of this clade have been found and these include the presence of membrane coat-like proteins, tubulin, sterol synthesis, and the presence of condensed DNA

4.
Synonym (taxonomy)
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For example, Linnaeus was the first to give a scientific name to the Norway spruce, which he called Pinus abies. This name is no longer in use, it is now a synonym of the current scientific name which is Picea abies, unlike synonyms in other contexts, in taxonomy a synonym is not interchangeable with the name of which it is a synonym. In taxonomy, synonyms are not equals, but have a different status, for any taxon with a particular circumscription, position, and rank, only one scientific name is considered to be the correct one at any given time. A synonym cannot exist in isolation, it is always an alternative to a different scientific name, given that the correct name of a taxon depends on the taxonomic viewpoint used a name that is one taxonomists synonym may be another taxonomists correct name. Synonyms may arise whenever the same taxon is described and named more than once, independently. They may also arise when existing taxa are changed, as when two taxa are joined to one, a species is moved to a different genus. To the general user of scientific names, in such as agriculture, horticulture, ecology, general science. A synonym is a name that was used as the correct scientific name but which has been displaced by another scientific name. Thus Oxford Dictionaries Online defines the term as a name which has the same application as another. In handbooks and general texts, it is useful to have mentioned as such after the current scientific name. Synonyms used in this way may not always meet the strict definitions of the synonym in the formal rules of nomenclature which govern scientific names. Changes of scientific name have two causes, they may be taxonomic or nomenclatural, a name change may be caused by changes in the circumscription, position or rank of a taxon, representing a change in taxonomic, scientific insight. A name change may be due to purely nomenclatural reasons, that is, based on the rules of nomenclature, the earliest such name is called the senior synonym, while the later name is the junior synonym. One basic principle of zoological nomenclature is that the earliest correctly published name, synonyms are important because if the earliest name cannot be used, then the next available junior synonym must be used for the taxon. Objective synonyms refer to taxa with the type and same rank. For example, John Edward Gray published the name Antilocapra anteflexa in 1855 for a species of pronghorn, however, it is now commonly accepted that his specimen was an unusual individual of the species Antilocapra americana published by George Ord in 1815. Ords name thus takes precedence, with Antilocapra anteflexa being a subjective synonym. Objective synonyms are common at the level of genera, because for various reasons two genera may contain the type species, these are objective synonyms

5.
Phylum
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In biology, a phylum is a taxonomic rank below kingdom and above class. Traditionally, in botany the term division was used instead of phylum, although from 1993 the International Code of Nomenclature for algae, fungi, depending on definitions, the kingdom Animalia contains approximately 35 phyla, Plantae contains about 12, and Fungi contains around 7. Current research in phylogenetics is uncovering the relationships between phyla, which are contained in larger clades, like Ecdysozoa and Embryophyta, the definitions of zoological phyla have changed from their origins in the six Linnaean classes and the four embranchements of Georges Cuvier. Haeckel introduced the term phylum, based on the Greek word phylon, in plant taxonomy, Eichler classified plants into five groups, named divisions. Informally, phyla can be thought of as grouping organisms based on general specialization of body plan, the most important objective measure in the above definitions is the certain degree—how unrelated do organisms need to be to be members of different phyla. The minimal requirement is that all organisms in a phylum should be more closely related to one another than to any other group. So phyla can be merged or split if it becomes apparent that they are related to one another or not, a definition of a phylum based on body plan has been proposed by paleontologists Graham Budd and Sören Jensen. By Budd and Jensens definition, a phylum is defined by a set of shared by all its living representatives. This approach brings some small problems—for instance, ancestral characters common to most members of a phylum may have been lost by some members, also, this definition is based on an arbitrary point of time, the present. However, as it is based, it is easy to apply to the fossil record. A greater problem is that it relies on a decision about which groups of organisms should be considered as phyla. However, proving that a fossil belongs to the group of a phylum is difficult. Furthermore, organisms in the group of a phylum can possess the body plan of the phylum without all the characteristics necessary to fall within it. This weakens the idea that each of the phyla represents a body plan. A classification using this definition may be affected by the chance survival of rare groups. Representatives of many modern phyla did not appear until long after the Cambrian, the kingdom Plantae is defined in various ways by different biologists. All definitions include the living embryophytes, to which may be added the two green algae divisions, Chlorophyta and Charophyta, to form the clade Viridiplantae. The table below follows the influential Cavalier-Smith system in equating Plantae with Archaeplastida, a group containing Viridiplantae, the definition and classification of plants at the division level also varies from source to source, and has changed progressively in recent years

6.
Brackish water
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Brackish water or briny water is water that has more salinity than fresh water, but not as much as seawater. It may result from mixing of seawater with fresh water, as in estuaries, the word comes from the Middle Dutch root brak. Brackish water is also the primary product of the salinity gradient power process. Because brackish water is hostile to the growth of most terrestrial plant species, without appropriate management it is damaging to the environment. Technically, brackish water contains between 0.5 and 30 grams of salt per litre—more often expressed as 0.5 to 30 parts per thousand, thus, brackish covers a range of salinity regimes and is not considered a precisely defined condition. It is characteristic of many brackish surface waters that their salinity can vary considerably over space and/or time, brackish water condition commonly occurs when fresh water meets seawater. In fact, the most extensive brackish water habitats worldwide are estuaries, the River Thames flowing through London is a classic river estuary. A similar pattern of replacement can be observed with the aquatic plants and this type of ecological succession from a freshwater to marine ecosystem is typical of river estuaries. Salmon are anadromous, meaning live in the sea but ascend rivers to spawn, eels are catadromous, living in rivers and streams. Besides the species migrate through estuaries, there are many other fish that use them as nursery grounds for spawning or as places young fish can feed. Herring and plaice are two commercially important species that use the Thames Estuary for this purpose, estuaries are also commonly used as fishing grounds, and as places for fish farming or ranching. Another important brackish water habitat is the swamp or mangal. Many, though not all, mangrove swamps fringe estuaries and lagoons where the salinity changes with each tide, like estuaries, mangrove swamps are extremely important breeding grounds for many fish, with species such as snappers, halfbeaks, and tarpon spawning or maturing among them. Mangroves represent important nesting site for numerous birds groups such as herons, storks, spoonbills, ibises, kingfishers, the Sundarbans and Bhitarkanika Mangroves are two of the large mangrove forests in the world, both on the coast of the Bay of Bengal. Some seas and lakes are brackish, the Baltic Sea is a brackish sea adjoining the North Sea. Because the salt water coming in from the sea is denser than freshwater, limited mixing occurs because of the lack of tides and storms, with the result that the fish fauna at the surface is freshwater in composition while that lower down is more marine. Cod are an example of a species found in deep water in the Baltic. The Caspian Sea is the worlds largest lake and contains brackish water with a salinity about one-third that of normal seawater, the Caspian is famous for its peculiar animal fauna, including one of the few non-marine seals and the great sturgeons, a major source of caviar

7.
Ocean
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An ocean is a body of saline water that composes much of a planets hydrosphere. On Earth, an ocean is one of the major divisions of the World Ocean. These are, in descending order by area, the Pacific, Atlantic, Indian, Southern, the word sea is often used interchangeably with ocean in American English but, strictly speaking, a sea is a body of saline water partly or fully enclosed by land. The ocean contains 97% of Earths water, and oceanographers have stated that less than 5% of the World Ocean has been explored, the total volume is approximately 1.35 billion cubic kilometers with an average depth of nearly 3,700 meters. As the world ocean is the component of Earths hydrosphere, it is integral to all known life, forms part of the carbon cycle. The world ocean is the habitat of 230,000 known species, but because much of it is unexplored, the origin of Earths oceans remains unknown, oceans are thought to have formed in the Hadean period and may have been the impetus for the emergence of life. Extraterrestrial oceans may be composed of water or other elements and compounds, the only confirmed large stable bodies of extraterrestrial surface liquids are the lakes of Titan, although there is evidence for the existence of oceans elsewhere in the Solar System. Early in their histories, Mars and Venus are theorized to have had large water oceans. The Mars ocean hypothesis suggests that nearly a third of the surface of Mars was once covered by water, compounds such as salts and ammonia dissolved in water lower its freezing point so that water might exist in large quantities in extraterrestrial environments as brine or convecting ice. Unconfirmed oceans are speculated beneath the surface of many planets and natural satellites, notably. The Solar Systems giant planets are thought to have liquid atmospheric layers of yet to be confirmed compositions. Oceans may also exist on exoplanets and exomoons, including surface oceans of water within a circumstellar habitable zone. Ocean planets are a type of planet with a surface completely covered with liquid. The concept of Ōkeanós has an Indo-European connection, Greek Ōkeanós has been compared to the Vedic epithet ā-śáyāna-, predicated of the dragon Vṛtra-, who captured the cows/rivers. Related to this notion, the Okeanos is represented with a dragon-tail on some early Greek vases, though generally described as several separate oceans, these waters comprise one global, interconnected body of salt water sometimes referred to as the World Ocean or global ocean. This concept of a body of water with relatively free interchange among its parts is of fundamental importance to oceanography. The major oceanic divisions – listed below in descending order of area and volume – are defined in part by the continents, various archipelagos, Oceans are fringed by smaller, adjoining bodies of water such as seas, gulfs, bays, bights, and straits. The Mid-Oceanic Ridge of the World are connected and form the Ocean Ridge, the continuous mountain range is 65,000 km long, and the total length of the oceanic ridge system is 80,000 km long

8.
Fresh water
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Fresh water is generally characterized by having low concentrations of dissolved salts and other total dissolved solids. The term specifically excludes seawater and brackish water although it does include mineral-rich waters such as chalybeate springs, the term sweet water has been used to describe fresh water in contrast to salt water. The term fresh water does not have the meaning as potable water. Much of the fresh water and ground water is unsuitable for drinking without some form of purification because of the presence of chemical or biological contaminants. It may also be in contact with the underlying underground water. The majority of water on Earth is in ice caps. The source of almost all water is precipitation from the atmosphere, in the form of mist, rain. Fresh water falling as mist, rain or snow contains materials dissolved from the atmosphere and material from the sea, in some cases this acid rain results in pollution of lakes and rivers. In coastal areas fresh water may contain significant concentrations of salts derived from the sea if windy conditions have lifted drops of seawater into the rain-bearing clouds. This can give rise to elevated concentrations of sodium, chloride, magnesium, significant quantities of iron may be transported in this way including the well-documented transfer of iron-rich rainfall falling in Brazil derived from sand-storms in the Sahara in north Africa. Water is an issue for the survival of all living organisms. Some can use water but many organisms including the great majority of higher plants. Out of all the water on Earth, saline water in oceans, seas and saline groundwater make up about 97% of it. Freshwater lakes contain about 87% of this surface water, including 29% in the African Great Lakes, 20% in Lake Baikal in Russia, 21% in the North American Great Lakes. Swamps have most of the balance only a small amount in rivers. In areas with no water on the ground surface, fresh water derived from precipitation may, because of its lower density. Most of the fresh water is frozen in ice sheets. Many areas suffer from lack of distribution of water, such as deserts

9.
Water
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Water is a transparent and nearly colorless chemical substance that is the main constituent of Earths streams, lakes, and oceans, and the fluids of most living organisms. Its chemical formula is H2O, meaning that its molecule contains one oxygen, Water strictly refers to the liquid state of that substance, that prevails at standard ambient temperature and pressure, but it often refers also to its solid state or its gaseous state. It also occurs in nature as snow, glaciers, ice packs and icebergs, clouds, fog, dew, aquifers, Water covers 71% of the Earths surface. It is vital for all forms of life. Only 2. 5% of this water is freshwater, and 98. 8% of that water is in ice and groundwater. Less than 0. 3% of all freshwater is in rivers, lakes, and the atmosphere, a greater quantity of water is found in the earths interior. Water on Earth moves continually through the cycle of evaporation and transpiration, condensation, precipitation. Evaporation and transpiration contribute to the precipitation over land, large amounts of water are also chemically combined or adsorbed in hydrated minerals. Safe drinking water is essential to humans and other even though it provides no calories or organic nutrients. There is a correlation between access to safe water and gross domestic product per capita. However, some observers have estimated that by 2025 more than half of the population will be facing water-based vulnerability. A report, issued in November 2009, suggests that by 2030, in developing regions of the world. Water plays an important role in the world economy, approximately 70% of the freshwater used by humans goes to agriculture. Fishing in salt and fresh water bodies is a source of food for many parts of the world. Much of long-distance trade of commodities and manufactured products is transported by boats through seas, rivers, lakes, large quantities of water, ice, and steam are used for cooling and heating, in industry and homes. Water is an excellent solvent for a variety of chemical substances, as such it is widely used in industrial processes. Water is also central to many sports and other forms of entertainment, such as swimming, pleasure boating, boat racing, surfing, sport fishing, Water is a liquid at the temperatures and pressures that are most adequate for life. Specifically, at atmospheric pressure of 1 bar, water is a liquid between the temperatures of 273.15 K and 373.15 K

10.
Budding
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Budding is a form of asexual reproduction in which a new organism develops from an outgrowth or bud due to cell division at one particular site. The new organism remains attached as it grows, separating from the parent organism only when it is mature, since the reproduction is asexual, the newly created organism is a clone and is genetically identical to the parent organism. Organisms such as hydra use regenerative cells for reproduction in the process of budding, in hydra, a bud develops as an outgrowth due to repeated cell division at one specific site. These buds develop into tiny individuals and, when mature, detach from the parent body. Internal budding or endodyogeny is a process of reproduction, favoured by parasites such as Toxoplasma gondii. It involves a process in which two daughter cells are produced inside a mother cell, which is then consumed by the offspring prior to their separation. Endopolygeny is the division into several organisms at once by internal budding, some cells divide asymmetrically by budding, for example Saccharomyces cerevisiae, the yeast species used in baking and brewing. This process results in a cell and a smaller daughter cell. Cryo-electron tomography recently revealed that mitochondria in cells divide by budding, in some multicellular animals, offspring may develop as outgrowths of the mother. Animals that reproduce by budding include corals, some sponges, some acoel flatworms, colonies of some bee species have also exhibited budding behavior, such as Apis dorsata. Although budding behavior is rare in this bee species, it has been observed when a group of workers leave the natal nest and construct a new nest usually near the natal one. In virology, budding is a form of viral shedding by which enveloped viruses acquire their external envelope from the host cell membrane, in agriculture and horticulture, budding refers to grafting the bud of one plant onto another

11.
Oval
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An oval is a closed curve in a plane which loosely resembles the outline of an egg. The term is not very specific, but in areas it is given a more precise definition. In common English, the term is used in a broader sense, the three-dimensional version of an oval is called an ovoid. The term oval when used to describe curves in geometry is not well-defined, many distinct curves are commonly called ovals or are said to have an oval shape. Generally, to be called an oval, a plane curve should resemble the outline of an egg or an ellipse, the adjectives ovoidal and ovate mean having the characteristic of being an ovoid, and are often used as synonyms for egg-shaped. In the theory of planes, an oval is a set of n +1 points in a projective plane of order n. An ovoid in the projective geometry PG is a set of q2 +1 points such that no three points are collinear. At each point of an all the tangent lines to the ovoid lie in a single plane. The shape of an egg is approximated by long half of a spheroid, joined to a short half of a roughly spherical ellipsoid. These are joined at the equator and sharing a principal axis of rotational symmetry, although the term egg-shaped usually implies a lack of reflection symmetry across the equatorial plane, it may also refer to true prolate ellipsoids. It can also be used to describe the 2-dimensional figure that, if revolved around its major axis, in technical drawing, an oval is a figure constructed from two pairs of arcs, with two different radii. The arcs are joined at a point in which lines tangential to both joining arcs lie on the line, thus making the joint smooth. Any point of an oval belongs to an arc with a constant radius, but in an ellipse, in common speech, oval means a shape rather like an egg or an ellipse, which may be two-dimensional or three-dimensional. It also often refers to a figure that resembles two semicircles joined by a rectangle, like a cricket infield, speed skating rink or an athletics track, however, this is more correctly called a stadium or archaically, an oblong. Sometimes, it can refer to any rectangle with rounded corners. The shape lends its name to many well-known places, ellipse Stadium Vesica piscis – a pointed oval

12.
Thomas Cavalier-Smith
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Thomas Cavalier-Smith, FRS, FRSC, NERC Professorial Fellow, is a Professor of Evolutionary Biology in the Department of Zoology, at the University of Oxford. He is well known for his system of classification of all organisms, Cavalier-Smith was born on 21 October 1941 in London. His parents were Alan Hailes Spencer and Mary Maude Cavalier-Smith and he was educated at Norwich School, Gonville and Caius College, Cambridge and Kings College London. He was under the supervision of Sir John Randall for his PhD thesis between 1964-1967, his thesis was entitled Organelle Development in Chlamydomonas reinhardii, from 1967 to 1969, he was a guest investigator at Rockefeller University. He became Lecturer of biophysics at King’s College London in 1969 and he was promoted to Reader in 1982. In 1989 he was appointed Professor of botany at the University of British Columbia, in 1999, he joined the University of Oxford, becoming Professor of evolutionary biology in 2000. He received the International Prize for Biology from the Emperor of Japan in 2004, and he was appointed Fellow of the Canadian Institute for Advanced Research between 1998-2007, and Advisor of the Integrated Microbial Biodiversity of CIFAR. He won the 2007 Frink Medal of the Zoological Society of London, Cavalier-Smith has written extensively on the taxonomy and classification of protists. One of his contributions to biology was his proposal of a new kingdom of life. He also introduced a new group for primitive eukarytes called the Chromalveolata, as well as Opisthokonta, Rhizaria, though fairly well known, many of his claims have been controversial and have not gained widespread acceptance in the scientific community to date. His taxonomic revisions often lead to changes in the classification of all life forms. Cavalier-Smiths first major classification system was the division of all organisms into eight kingdoms, in 1993, he revised his system particularly in the light of the general acceptance of Archaebacteria as separate group from Bacteria. In addition, some protists lacking mitochondria were discovered, as a result, these amitochondriate protists were separated from the protist kingdom, giving rise to the, at the same time, superkingdom and kingdom Archezoa. This was known as the Archezoa hypothesis, the eight kingdoms became, Eubacteria, Archaebacteria, Archezoa, Protozoa, Chromista, Plantae, Fungi, and Animalia. However, kingdom Archezoa is now defunct and he now assigns former members of the kingdom Archezoa to the phylum Amoebozoa. By 1998, Cavalier-Smith had reduced the number of kingdoms from eight to six, Animalia, Protozoa, Fungi, Plantae, Chromista. He created three new animal phyla, Acanthognatha, Brachiozoa, and Lobopoda and recognized a total of 23 animal phyla, in this scheme they reintroduced the division of prokaryotes into two kingdoms, Bacteria and Archaea. This is based on the consensus in the Taxonomic Outline of Bacteria and Archaea, in 2006, Cavalier-Smith proposed that the last universal common ancestor to all life was a non-flagellate negibacterium with two membranes

13.
Gracilicutes
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Gracilicutes is a controversial taxon in bacterial taxonomy. This taxon was revived in 2006 by Cavalier-Smith as an infrakindgom containing the phyla Spirochaetae, Sphingobacteria, Planctobacteria, however, this taxon is not generally accepted and the three-domain system is followed. It is a clade that branched off from other bacteria just before the evolutionary loss of the outer membrane or capsule. The following graph shows Cavalier-Smiths version of the tree of life, indicating the status of Gracilicutes

14.
Peptidoglycan
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Peptidoglycan, also known as murein, is a polymer consisting of sugars and amino acids that forms a mesh-like layer outside the plasma membrane of most bacteria, forming the cell wall. The sugar component consists of alternating residues of β- linked N-acetylglucosamine, attached to the N-acetylmuramic acid is a peptide chain of three to five amino acids. The peptide chain can be cross-linked to the chain of another strand forming the 3D mesh-like layer. Peptidoglycan serves a role in the bacterial cell wall, giving structural strength. Peptidoglycan is also involved in binary fission during bacterial cell reproduction, the peptidoglycan layer is substantially thicker in gram-positive bacteria than in gram-negative bacteria, with the attachment of the S-layer. Peptidoglycan forms around 90% of the dry weight of gram-positive bacteria, thus, presence of high levels of peptidoglycan is the primary determinant of the characterisation of bacteria as gram-positive. In gram-positive strains, it is important in attachment roles and serotyping purposes, for both gram-positive and gram-negative bacteria, particles of approximately 2 nm can pass through the peptidoglycan. The peptidoglycan layer in the cell wall is a crystal lattice structure formed from linear chains of two alternating amino sugars, namely N-acetylglucosamine and N-acetylmuramic acid. The alternating sugars are connected by a β--glycosidic bond, peptidoglycan is one of the most important sources of D-amino acids in nature. Cross-linking between amino acids in different linear amino sugar chains occurs with the help of the enzyme DD-transpeptidase and results in a 3-dimensional structure that is strong, the specific amino acid sequence and molecular structure vary with the bacterial species. The peptidoglycan monomers are synthesized in the cytosol and are attached to a membrane carrier bactoprenol. Bactoprenol transports peptidoglycan monomers across the membrane where they are inserted into the existing peptidoglycan. In the first step of peptidoglycan synthesis, the glutamine, which is an acid, donates an amino group to a sugar. This turns fructose 6-phosphate into glucosamine-6-phosphate, in step two, an acetyl group is transferred from acetyl CoA to the amino group on the glucosamine-6-phosphate creating N-acetyl-glucosamine-6-phosphate. In step three of the process, the N-acetyl-glucosamine-6-phosphate is isomerized, which will change N-acetyl-glucosamine-6-phosphate to N-acetyl-glucosamine-1-phosphate. In step 4, the N-acetyl-glucosamine-1-phosphate, which is now a monophosphate, uridine triphosphate, which is a pyrimidine nucleotide, has the ability to act as an energy source. In this particular reaction, after the monophosphate has attacked the UTP and this initial stage, is used to create the precursor for the NAG in peptidoglycan. In step 5, some of the UDP-N-acetylglucosamine is converted to UDP-MurNAc by the addition of a group to the glucosamine

15.
Cell wall
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A cell wall is a structural layer surrounding some types of cells, situated outside the cell membrane. It can be tough, flexible, and sometimes rigid and it provides the cell with both structural support and protection, and also acts as a filtering mechanism. Cell walls are present in most prokaryotes, in algae, plants and fungi, a major function is to act as pressure vessels, preventing over-expansion of the cell when water enters. The composition of cell walls varies between species and may depend on type and developmental stage. The primary cell wall of plants is composed of the polysaccharides cellulose, hemicellulose. Often, other such as lignin, suberin or cutin are anchored to or embedded in plant cell walls. Algae possess walls made of glycoproteins and polysaccharides such as carrageenan, in bacteria, the cell wall is composed of peptidoglycan. The cell walls of archaea have various compositions, and may be formed of glycoprotein S-layers, pseudopeptidoglycan, Fungi possess cell walls made of the glucosamine polymer chitin. Unusually, diatoms have a wall composed of biogenic silica. A plant cell wall was first observed and named by Robert Hooke in 1665, in 1804, Karl Rudolphi and J. H. F. Link proved that cells had independent cell walls, before, it had been thought that cells shared walls and that fluid passed between them this way. The mode of formation of the wall was controversial in the 19th century. Hugo von Mohl advocated the idea that the wall grows by apposition. Carl Nägeli believed that the growth of the wall in thickness, each theory was improved in the following decades, the apposition theory by Eduard Strasburger, and the intussusception theory by Julius Wiesner. In 1930, Ernst Münch coined the term apoplast in order to separate the living symplast from the dead plant region, Cell walls serve similar purposes in those organisms that possess them. They may give cells rigidity and strength, offering protection against mechanical stress, in multicellular organisms, they permit the organism to build and hold a definite shape. Cell walls also limit the entry of large molecules that may be toxic to the cell and they further permit the creation of stable osmotic environments by preventing osmotic lysis and helping to retain water. Their composition, properties, and form may change during the cell cycle, in most cells, the cell wall is flexible, meaning that it will bend rather than holding a fixed shape, but has considerable tensile strength

16.
Copolymer
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When two or more different monomers unite together to polymerize, their result is called a copolymer and its process is called copolymerization. Commercially relevant copolymers include acrylonitrile butadiene styrene, styrene/butadiene co-polymer, nitrile rubber, styrene-acrylonitrile, styrene-isoprene-styrene, since a copolymer consists of at least two types of constituent units, copolymers can be classified based on how these units are arranged along the chain. Block copolymers comprise two or more homopolymer subunits linked by covalent bonds, the union of the homopolymer subunits may require an intermediate non-repeating subunit, known as a junction block. Block copolymers with two or three blocks are called diblock copolymers and triblock copolymers, respectively. Copolymers may also be described in terms of the existence of or arrangement of branches in the polymer structure, linear copolymers consist of a single main chain whereas branched copolymers consist of a single main chain with one or more polymeric side chains. Other special types of branched copolymers include star copolymers, brush copolymers, in gradient copolymers the monomer composition changes gradually along the chain. A terpolymer is a copolymer consisting of three distinct monomers, the term is derived from ter, meaning thrice, and polymer. Stereoblock copolymers A special structure can be formed from one monomer where now the distinguishing feature is the tacticity of each block, statistical copolymers are dictated by the reaction kinetics of the two chemically distinct monomer reactants, and are commonly referred to interchangeably as “random” in the polymer literature. As with other types of copolymers, random copolymers can have interesting, examples of commercially relevant random copolymers include rubbers made from styrene-butadiene copolymers and resins from styrene-acrylic or methacrylic acid derivatives. A number of parameters are relevant in the composition of the product, namely. Reactivity ratios describe whether the monomer reacts preferentially with a segment of the type or of the other type. For example, a reactivity ratio that is less one for component 1 indicates that this component reacts with the other type of monomer more readily. When both reactivity ratios are less than one, there is a point in the Mayo-Lewis plot. At this point, the fraction of monomer equals the composition of the component in the polymer. There are several ways to synthesize random copolymers, free radical polymerization is less expensive than other methods, and produces high-molecular weight polymer quickly. Several methods offer better control over dispersity, additionally, anionic polymerization is expensive and requires very clean reaction conditions, and is therefore difficult to implement on a large scale. These methods are favored over anionic polymerization because they can be performed in similar to free radical polymerization. The reactions require longer periods than free radical polymerization

17.
Glycoprotein
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Glycoproteins are proteins that contain oligosaccharide chains covalently attached to polypeptide side-chains. The carbohydrate is attached to the protein in a cotranslational or posttranslational modification and this process is known as glycosylation. Secreted extracellular proteins are often glycosylated, in proteins that have segments extending extracellularly, the extracellular segments are also often glycosylated. Glycoproteins are also often important integral membrane proteins, where they play a role in cell–cell interactions and it is important to distinguish endoplasmic reticulum-based glycosylation of the secretory system without reversible cytosolic-nuclear glycosylation. In contrast, classical secretory glycosylation can be structurally essential, for example, inhibition of asparagine-linked, i. e. N-linked, glycosylation can prevent glycoprotein folding and full inhibition can be toxic to an individual cell. In contrast, perturbation of terminal processing, which occurs in the Golgi apparatus, is dispensable for isolated cells but can lead to human disease, a famous example of this latter effect is the ABO blood system. There are several types of glycosylation, although the first two are the most common, in N-glycosylation, sugars are attached to nitrogen, typically on the amide side-chain of asparagine. In O-glycosylation, sugars are attached to oxygen, typically on serine or threonine, in P-glycosylation, sugars are attached to phosphorus on a phosphoserine. In C-glycosylation, sugars are attached directly to carbon, such as in the addition of mannose to tryptophan, in glypiation, a GPI glycolipid is attached to the C-terminus of a polypeptide, serving as a membrane anchor. Monosaccharides commonly found in eukaryotic glycoproteins include, The sugar group can assist in protein folding or improve proteins stability, one example of glycoproteins found in the body is mucins, which are secreted in the mucus of the respiratory and digestive tracts. The sugars when attached to give them considerable water-holding capacity. Glycoproteins are important for blood cell recognition, especially in mammals. Examples of glycoproteins in the system are, molecules such as antibodies. Molecules of the major histocompatibility complex, which are expressed on the surface of cells, sialyl Lewis X antigen on the surface of leukocytes. H antigen of the ABO blood compatibility antigens, other examples of glycoproteins include, glycoprotein IIb/IIIa, an integrin found on platelets that is required for normal platelet aggregation and adherence to the endothelium. Components of the zona pellucida, which surrounds the oocyte, and is important for sperm-egg interaction, structural glycoproteins, which occur in connective tissue. These help bind together the fibers, cells, and ground substance of connective tissue and they may also help components of the tissue bind to inorganic substances, such as calcium in bone. Glycoprotein-41 and glycoprotein-120 are HIV viral coat proteins, soluble glycoproteins often show a high viscosity, for example, in egg white and blood plasma

18.
Glutamic acid
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Glutamic acid is an α-amino acid with formula C 5H 9O 4N. It is usually abbreviated as Glu or E in biochemistry and its molecular structure could be idealized as HOOC-CH-2-COOH, with two carboxyl groups -COOH and one amino group -NH2. However, in the state and mildly acid water solutions. Glutamic acid is used by almost all living beings in the biosynthesis of proteins and it is non-essential in humans, meaning the body can synthesize it. The acid can lose one proton from second carboxyl group to form the conjugate base and this form of the compound is prevalent in neutral solutions. The glutamate neurotransmitter plays the role in neural activation. This anion is also responsible for the flavor of certain foods. In highly alkaline solutions the doubly negative anion −OOC-CH-2-COO− prevails, the radical corresponding to glutamate is called glutamyl. When glutamic acid is dissolved in water, the group may gain a proton, and/or the carboxyl groups may lose protons. In sufficiently acid environments, the group gains a proton. At pH values between about 2.5 and 4.1, the carboxylic acid closer to the amine generally loses a proton, and the acid becomes the neutral zwitterion −OOC-CH-2-COOH. This is also the form of the compound in the solid state. The switchover is gradual, the two forms are in equal concentrations at pH2.10, at even higher pH, the other carboxyl loses its proton and the acid exists almost entirely as the glutamate anion −OOC-CH-2-COO−, with a single negative charge. The switchover occurs at pH4.07, the latter is the case, in particular, in the physiological pH range. At even higher pH, the group loses the extra proton. The switchover occurs at pH9.47, the carbon atom adjacent to the amino group is chiral, so glutamic acid can exist in two optical isomers, D and L. The L form is the one most widely occurring in nature, but the D form occurs in special contexts, such as the cell walls of the bacterium Escherichia coli. Although they occur naturally in foods, the flavor contributions made by glutamic acid

19.
Bacterial cellular morphologies
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Bacteria are classified by direct examination with the light microscope through its morphology and aggregation. The basic forms are spheres and round-ended cylinders, but there may be others such as helically twisted cylinders, cylinders curved in one plane and unusual morphologies. They also conform diplos, tetrads, staphylos, streptos, palizadas etc, a coccus is any microorganism whose overall shape is spherical or nearly spherical. Describing a bacterium as a coccus, or sphere, distinguishes it from bacillus and this is the first of many taxonomic traits for identifying and classifying a bacterium according to binomial nomenclature. Examples are Streptococcus pneumoniae, Moraxella catarrhalis, Neisseria gonorrhoeae and Neisseria meningitidis and its name comes from diplo, meaning double, and coccus, meaning berry. This is because berries are round, like a diplococcus, in former times, a bacterial genus Diplococcus was recognized, but it is not used anymore. A coccobacillus is a type of rod-shaped bacteria, the word coccobacillus reflects an intermediate shape between coccus and bacillus. Coccobacilli rods are so short and wide that they resemble cocci, haemophilus influenzae and Chlamydia trachomatis are coccobacilli. Aggregatibacter actinomycetemcomitans is a gram negative coccobacillus which is prevalent in subgingival plaques, acinetobacter strains may grow on solid media as coccobacilli. Coxiella burnetti is also a coccobacillus, a bacillus is a rod-shaped bacterium. There is no connection between the shape of a bacterium and its colors in the Gram staining, bacilli usually divide in the same plane and are solitary, but can combine to form diplobacilli, streptobacilli, and palisades. Diplobacilli, Two bacilli arranged side by side each other. Coccobacillus, Oval and similar to coccus, spiral bacteria form the third major bacterial cell morphology. Spiral bacteria can be sub-classified as spirilla, spirochetes, or vibrios based on the number of twists per cell, cell thickness, cell flexibility, bacterial morphological plasticity Bacteria Picture Gallery

20.
Cell membrane
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The cell membrane is a biological membrane that separates the interior of all cells from the outside environment. The cell membrane is permeable to ions and organic molecules and controls the movement of substances in. The basic function of the membrane is to protect the cell from its surroundings. It consists of the bilayer with embedded proteins. Cell membranes can be artificially reassembled, Some authors that did not believe that there was a functional permeable boundary at the surface of the cell preferred to use the term plasmalemma to the extern region of the cell. The cell membrane surrounds the cytoplasm of living cells, physically separating the components from the extracellular environment. The cell membrane also plays a role in anchoring the cytoskeleton to provide shape to the cell, fungi, bacteria, most archaea, and plants also have a cell wall, which provides a mechanical support to the cell and precludes the passage of larger molecules. The cell membrane is permeable and able to regulate what enters and exits the cell. The movement of substances across the membrane can be passive, occurring without the input of cellular energy, or active. The membrane also maintains the cell potential, the cell membrane thus works as a selective filter that allows only certain things to come inside or go outside the cell. The cell employs a number of mechanisms that involve biological membranes,1. Passive osmosis and diffusion, Some substances such as carbon dioxide and oxygen, can move across the membrane by diffusion. Because the membrane acts as a barrier for certain molecules and ions, such a concentration gradient across a semipermeable membrane sets up an osmotic flow for the water. Transmembrane protein channels and transporters, Nutrients, such as sugars or amino acids, must enter the cell, such molecules diffuse passively through protein channels such as aquaporins in facilitated diffusion or are pumped across the membrane by transmembrane transporters. Protein channel proteins, also called permeases, are quite specific, recognizing and transporting only a limited food group of chemical substances. Endocytosis, Endocytosis is the process in which cells absorb molecules by engulfing them, the plasma membrane creates a small deformation inward, called an invagination, in which the substance to be transported is captured. The deformation then pinches off from the membrane on the inside of the cell, Endocytosis is a pathway for internalizing solid particles, small molecules and ions, and macromolecules. Endocytosis requires energy and is thus a form of active transport and this is the process of exocytosis

21.
Electron tomography
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Electron tomography is a tomography technique for obtaining detailed 3D structures of sub-cellular macro-molecular objects. Electron tomography is an extension of traditional transmission electron microscopy and uses an electron microscope to collect the data. In the process, a beam of electrons is passed through the sample at incremental degrees of rotation around the center of the target sample and this information is collected and used to assemble a three-dimensional image of the target. In the field of biology, bright-field transmission electron microscopy and high-resolution TEM are the primary imaging methods for tomography tilt series acquisition, however, there are two issues associated with BF-TEM and HRTEM. First, acquiring an interpretable 3-D tomogram requires that the image intensities vary monotonically with material thickness. ADF-STEM also acts as a filter, eliminating the edge-enhancing artifacts common in BF/HRTEM. For 3D imaging, the resolution is described by the Crowther criterion. In 2010, a 3D resolution of 0. 5±0. 1×0. 5±0. 1×0. 7±0.2 nm was achieved with a single-axis ADF-STEM tomography, recently, atomic resolution in 3D electron tomography reconstructions has been demonstrated. ADF-STEM tomography has recently used to directly visualize the atomic structure of screw dislocations in nanoparticles. The most popular tilting methods are the single-axis and the dual-axis tilting methods, the geometry of most specimen holders and electron microscopes normally precludes tilting the specimen through a full 180° range, which can lead to artifacts in the 3D reconstruction of the target. By using dual-axis tilting, the artifacts are reduced by a factor of 2 compared to single-axis tilting. However, twice as many images need to be taken, another method of obtaining a tilt-series is the so-called conical tomography method, in which the sample is tilted, and then rotated a complete turn. Tomography Tomographic reconstruction Cryo-electron tomography Positron emission tomography Crowther criterion X-ray computed tomography tomviz tomography software imod tomography software

22.
Gram-negative bacteria
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Gram-negative bacteria are a group of bacteria that do not retain the crystal violet stain used in the Gram staining method of bacterial differentiation. They are characterized by their cell envelopes, which are composed of a peptidoglycan cell wall sandwiched between an inner cytoplasmic cell membrane and a bacterial outer membrane. Gram-negative bacteria are spread worldwide, in all environments that support life. Several classes of antibiotics target gram-negative bacteria specifically, including aminoglycosides, historically, the kingdom Monera was divided into four divisions based on Gram staining, Firmacutes, Gracillicutes, Mollicutes and Mendocutes. Since 1987, the monophyly of the bacteria has been disproven with molecular studies. However some authors, such as Cavalier-Smith still treat them as a monophyletic taxon, bacteria are traditionally divided into the two groups, gram-positive and gram-negative, based on their Gram stain retention. These groups are thought of as lineages, with gram-negative bacteria more closely related to one another than to gram-positive bacteria. While this is true, the classification system breaks down in some cases. A given bacterias Gram stain result, bacterial membrane organization, as such, the Gram stain cannot be reliably used to assess familial relationships of bacteria. That said, Gram staining does often give information about the composition of the cell membrane. Of these two distinct groups of prokaryotic organisms, monoderm prokaryotes are indicated to be ancestral. In addition, a number of taxa that are either part of the phylum Firmicutes or branches in its proximity are also found to possess a diderm cell structure. Other notable groups of bacteria include the cyanobacteria, spirochaetes, green sulfur. Medically relevant gram-negative cocci include the four types that cause a sexually transmitted disease, a meningitis, medically relevant gram-negative bacilli include a multitude of species. Some of them cause primarily respiratory problems, primarily urinary problems, transformation is one of three processes for horizontal gene transfer, in which exogenous genetic material passes from bacterium to another, the other two being conjugation and transduction. In transformation, the material passes through the intervening medium. One of the unique characteristics of gram-negative bacteria is the structure of the bacterial outer membrane. The outer leaflet of this comprises a complex lipopolysaccharide whose lipid portion acts as an endotoxin

23.
Cytoplasm
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In cell biology, the cytoplasm is the material within a living cell, excluding the cell nucleus. It comprises cytosol and the organelles – the cells internal sub-structures, all of the contents of the cells of prokaryotic organisms are contained within the cytoplasm. Within the cells of organisms the contents of the cell nucleus are separated from the cytoplasm. The cytoplasm is about 80% water and usually colorless, the submicroscopic ground cell substance or cytoplasmatic matrix which remains after exclusion the cell organelles and particles is groundplasm. It is within the cytoplasm that most cellular activities occur, such as many metabolic pathways including glycolysis, the concentrated inner area is called the endoplasm and the outer layer is called the cell cortex or the ectoplasm. Movement of calcium ions in and out of the cytoplasm is an activity for metabolic processes. In plants, movement of the cytoplasm around vacuoles is known as cytoplasmic streaming, the term was introduced by Rudolf von Kölliker in 1863, originally as a synonym for protoplasm, but later it has come to mean the cell substance and organelles outside the nucleus. There has been disagreement on the definition of cytoplasm, as some authors prefer to exclude from it some organelles. The physical properties of the cytoplasm have been contested in recent years and it remains uncertain how the varied components of the cytoplasm interact to allow movement of particles and organelles while maintaining the cell’s structure. The flow of cytoplasmic components plays an important role in cellular functions which are dependent on the permeability of the cytoplasm. An example of function is cell signalling, a process which is dependent on the manner in which signaling molecules are allowed to diffuse across the cell. While small signaling molecules like calcium ions are able to diffuse with ease, larger molecules, the irregular dynamics of such particles have given rise to various theories on the nature of the cytoplasm. There has long been evidence that the cytoplasm behaves like a sol-gel and it is thought that the component molecules and structures of the cytoplasm behave at times like a disordered colloidal solution and at other times like an integrated network, forming a solid mass. Recently it has proposed that the cytoplasm behaves like a glass-forming liquid approaching the glass transition. A cells ability to vitrify in the absence of activity, as in dormant periods. There has been examining the motion of cytoplasmic particles independent of the nature of the cytoplasm. In such an approach, the aggregate random forces within the cell caused by motor proteins explain the non-Brownian motion of cytoplasmic constituents. The three major elements of the cytoplasm are the cytosol, organelles and inclusions, the cytosol is the portion of the cytoplasm not contained within membrane-bound organelles

24.
Periplasm
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The periplasm is a concentrated gel-like matrix in the space between the inner cytoplasmic membrane and the bacterial outer membrane called the periplasmic space in gram-negative bacteria. It has been found using cryo-electron microscopy, that a much smaller periplasmic space is present in gram-positive bacteria, the periplasm may constitute up to 40% of the total cell volume of gram-negative bacteria, and this is a much smaller percentage in gram-positive bacteria. These bacteria are distinguished from each other based on the presence or absence of a lipid membrane. All gram-positive bacteria are bounded by a single unit lipid membrane, for the bacterial cells that are bounded by a single cell membrane the term monoderm bacteria or monoderm prokaryotes has been proposed. The presence of inner and outer cell membranes forms and define the periplasmic space or periplasmic compartment. These bacterial cells with two membranes have been designated as diderm bacteria, the distinction between the monoderm and diderm prokaryotes is supported by conserved signature indels in a number of important proteins. In diderm bacteria, the contains a thin cell wall composed of peptidoglycan. Importantly, the periplasm is devoid of ATP, D. White, The Physiology and Biochemistry of Prokaryotes, Oxford University Press, Oxford,2000, pp.22

25.
Sterol
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Sterols, also known as steroid alcohols, are a subgroup of the steroids and an important class of organic molecules. They occur naturally in plants, animals, and fungi, with the most familiar type of animal sterol being cholesterol, cholesterol is vital to animal cell membrane structure and function as a precursor to fat-soluble vitamins and steroid hormones. Sterols of plants are called phytosterols and sterols of animals are called zoosterols, the most important zoosterol is cholesterol, notable phytosterols include campesterol, sitosterol, and stigmasterol. Ergosterol is a present in the cell membrane of fungi. Preliminary research has shown that phytosterols may have anticancer effects, Sterols and related compounds play essential roles in the physiology of eukaryotic organisms. For example, cholesterol forms part of the membrane in animals. In humans and other animals, corticosteroids, such as cortisol act as signaling compounds in cellular communication, Sterols are common components of human skin oils. Sterols are a subgroup of steroids with a group at the 3-position of the A-ring. They are amphipathic lipids synthesized from acetyl-coenzyme A via the HMG-CoA reductase pathway, the overall molecule is quite flat. The hydroxyl group on the A ring is polar, the rest of the aliphatic chain is non-polar. Cholesterol Ergosterol Hopanoids Phytosterol Steroids Alberts, Bruce, the Fluidity of a Lipid Bilayer Depends on Its Composition Sterols Cyberlipid. org

26.
Endocytosis
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Endocytosis is a form of active transport in which a cell transports molecules into the cell by engulfing them in an energy-using process. The term was proposed by De Duve in 1963, phagocytosis was discovered by Élie Metchnikoff. Endocytosis pathways can be subdivided into four categories, namely, receptor-mediated endocytosis, caveolae, macropinocytosis, clathrin-mediated endocytosis is mediated by the production of small vesicles that have a morphologically characteristic coat made up of the cytosolic protein clathrin. Clathrin-coated vesicles are found in all cells and form domains of the plasma membrane termed clathrin-coated pits. Caveolae are the most common reported non-clathrin-coated plasma membrane buds, which exist on the surface of many and they consist of the cholesterol-binding protein caveolin with a bilayer enriched in cholesterol and glycolipids. Caveolae are small pits in the membrane that resemble the shape of a cave. Uptake of extracellular molecules is also believed to be mediated via receptors in caveolae. Potocytosis is a form of receptor-mediated endocytosis that uses caveolae vesicles to bring molecules of various sizes into the cell, unlike most endocytosis that uses caveolae to deliver contents of vesicles to lysosomes or other organelles, material endocytosed via potocytosis is released into the cytosol. The filling of the pocket occurs in a non-specific manner, the vesicle then travels into the cytosol and fuses with other vesicles such as endosomes and lysosomes. These processes involve the uptake of larger areas than clathrin-mediated endocytosis. The principal components of the pathway are, Early endosomes are the first compartment of the endocytic pathway. Early endosomes are often located in the periphery of the cell and they have a characteristic tubulo-vesicular structure and a mildly acid pH. It is also the site of sorting into transcytotic pathway to later compartments via transvesicular compartments, late endosomes often contain proteins characteristic of lysosomes, including lysosomal membrane glycoproteins and acid hydrolases. They are acidic, and are part of the pathway of mannose-6-phosphate receptors. Late endosomes are thought to mediate a final set of sorting events prior to delivery of material to lysosomes, lysosomes are the last compartment of the endocytic pathway. Their chief function is to break down waste products, fats, carbohydrates, proteins. These are then returned to the cytoplasm as new cell-building materials, the approximate pH of a lysosome is 4.8 and by electron microscopy usually appear as large vacuoles containing electron dense material. They have a content of lysosomal membrane proteins and active lysosomal hydrolases

27.
Conserved signature indels
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Conserved signature inserts and deletions in protein sequences provide an important category of molecular markers for understanding phylogenetic relationships. While indels can be arbitrary inserts or deletions, CSIs are defined as only those protein indels that are present within conserved regions of the protein, the CSIs that are restricted to a particular clade or group of species, generally provide good phylogenetic markers of common evolutionary descent. Due to the rarity and highly specific nature of such changes, other confounding factors such as differences in evolutionary rates at different sites or among different species also generally do not affect the interpretation of a CSI. Most CSIs that have identified have been found to exhibit high predictive value. Therefore, based upon their presence or absence, it should be possible to both known and even previously unknown species belonging to these groups in different environments. Group specific CSIs are commonly shared by different species belonging to a particular Taxon and these CSIs were most likely introduced in an ancestor of the group of species before the members of the taxa diverged. They provide molecular means for distinguishing members of a taxon from all other organisms. Figure 1 shows an example of 5aa CSI found in all species belonging to the taxon X and this is a distinctive characteristic of this taxon as it is not found in any other species. This signature was introduced in a common ancestor of the species from this taxon. Similarly other group-specific signatures could be shared by either A1 and A2 or B1 and B2, etc. or even by X1 and X2 or by X3 and X4, etc. The groups A, B, C, D and X, group specific CSIs have been used in the past to determine the phylogenetic relationship of a number of bacterial phyla and subgroups within it. For example a 3 amino acid insert was uniquely shared by members of the phylum Thermotogae in the essential 50S ribosomal protein L7/L12 and this is not present in any other bacteria species and could be used to characterize members of the phylum Thermotogae from all other bacteria. Group specific CSIs were also used to characterize subgroups within the phylum Thermotogae, main-line CSIs are those in which a conserved insert or deletion is shared by several major phyla, but absent from other phyla. Figure 2 shows an example of 5aa CSI found in a region that is commonly present in the species belonging to phyla X, Y and Z. This signature indicates a relationship of taxa X, Y and Z. Main-line CSIs have been used in the past to determine the relationship of a number of bacterial phyla. The large CSI of about 150-180 amino acids within a region of Gyrase B, is commonly shared between various Proteobacteria, Chlamydiales, Planctomycetes and Aquificales species. This CSI is absent in other bacterial phyla as well as Archaea

28.
Biological life cycle
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In biology, a biological life cycle is a series of changes in form that an organism undergoes, returning to the starting state. The concept is related to those of the life history, development and ontogeny. Transitions of form may involve growth, asexual reproduction, and/or sexual reproduction, in some organisms, different generations of the species succeed each other during the life cycle. For plants and many algae, there are two stages, and the life cycle is referred to as alternation of generations. The term life history is used, particularly for organisms such as the red algae which have three multicellular stages, rather than two. Life cycles that include sexual reproduction involve alternating haploid and diploid stages, to return from a diploid stage to a haploid stage, meiosis must occur. In regard to changes of ploidy, there are 3 types of cycles, haplontic life cycle — the haploid stage is multicellular, diplontic life cycle — the diploid stage is multicellular and haploid gametes are formed, meiosis is gametic. Haplodiplontic life cycle — multicellular diploid and haploid stages occur, meiosis is sporic, the cycles differ in when mitosis occurs. Zygotic meiosis and gametic meiosis have one stage, mitosis occurs during the n phase in zygotic meiosis. Therefore, zygotic and gametic meiosis are collectively termed haplobiontic, sporic meiosis, on the other hand, has mitosis in two stages, both the diploid and haploid stages, termed diplobiontic. The study of reproduction and development in organisms was carried out by botanists and zoologists. Wilhelm Hofmeister demonstrated that alternation of generations is a feature that unites plants, some terms used for the description of life cycles were proposed initially for algae by Nils Svedelius, and then became used for other organisms. Other terms used in protist life cycles were introduced by Karl Gottlieb Grell, the description of the complex life cycles of various organisms contributed to the disproof of the ideas of spontaneous generation in the 1840s and 1850s. A zygotic meiosis is a meiosis of a zygote immediately after karyogamy and this way, the organism ends its diploid phase and produces several haploid cells. These cells divide mitotically to form larger, multicellular individuals. Two opposite types of gametes from these individuals or cells fuse to become a zygote, in the whole cycle, zygotes are the only diploid cell, mitosis occurs only in the haploid phase. The individuals or cells as a result of mitosis are haplonts, haplonts are, In archaeplastidans, some green algae In stramenopiles, some golden algae In alveolates, many dinoflagellates eg. Cells from the individuals then undergo meiosis to produce haploid cells or gametes

29.
Sessility (motility)
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In biology, sessility refers to organisms that do not possess a means of self-locomotion and are normally immobile. This is distinct from the meaning of sessility which refers to an organism or biological structure attached directly by its base without a stalk. Sessile organisms can move through outside sources but are permanently attached to something. Organisms such as corals lay down their own substrate from which they grow, other organisms grow from a solid such as a rock, dead tree trunk, or a manmade object such as a buoy or ships hull. Sessile animals typically have a phase in their development. Sponges have a larval stage, which becomes sessile at maturity. In contrast, many jellyfish develop as sessile polyps early in their life cycle, in the case of the cochineal, it is in the nymph stage that the cochineal disperses. The juveniles move to a spot and produce long wax filaments. Later they move to the edge of the cactus pad where the wind catches the wax filaments, many sessile animals, including sponges, corals and hydra, are capable of asexual reproduction in situ by the process of budding. Sessile organisms such as barnacles and tunicates need some mechanism to move their young into new territory and this is why the most widely accepted theory explaining the evolution of a larval stage is the need for long-distance dispersal ability. This allows for faster reproduction and better protection from predators, the circalittoral zone of coastal environments and biomes are dominated by sessile organisms such as oysters. Carbonate platforms grow due to the buildup of skeletal remains of organisms, usually microorganisms. In anatomy and botany, sessility refers to an organism or biological structure that has no peduncle or stalk, a sessile structure has no stalk

30.
Flagellum
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A flagellum is a lash-like appendage that protrudes from the cell body of certain prokaryotic and eukaryotic cells. The word flagellum in Latin means whip, the primary role of the flagellum is locomotion, but it also often has function as a sensory organelle, being sensitive to chemicals and temperatures outside the cell. Flagella are organelles defined by function rather than structure, large differences occur between different types of flagella, the prokaryotic and eukaryotic flagella differ greatly in protein composition, structure, and mechanism of propulsion. However, both can be used for swimming, an example of a flagellated bacterium is the ulcer-causing Helicobacter pylori, which uses multiple flagella to propel itself through the mucus lining to reach the stomach epithelium. An example of a eukaryotic cell is the mammalian sperm cell. Eukaryotic flagella are structurally identical to eukaryotic cilia, although distinctions are made according to function and/or length. Fimbriae and pili are also thin appendages, but have different functions and are usually smaller, three types of flagella have so far been distinguished, bacterial, archaeal, and eukaryotic. The main differences among these three types are, Bacterial flagella are helical filaments, each with a motor at its base which can turn clockwise or counterclockwise. They provide two of several kinds of bacterial motility, archaeal flagella are superficially similar to bacterial flagella, but are different in many details and considered non-homologous. Eukaryotic flagella—those of animal, plant, and protist cells—are complex cellular projections that lash back, eukaryotic flagella are classed along with eukaryotic motile cilia as undulipodia to emphasize their distinctive wavy appendage role in cellular function or motility. Primary cilia are immotile, and are not undulipodia, they have a structurally different 9+0 axoneme rather than the 9+2 axoneme found in both flagella and motile cilia undulipodia, the bacterial flagellum is made up of the protein flagellin. Its shape is a 20-nanometer-thick hollow tube and it is helical and has a sharp bend just outside the outer membrane, this hook allows the axis of the helix to point directly away from the cell. A shaft runs between the hook and the body, passing through protein rings in the cells membrane that act as bearings. Gram-positive organisms have two of these basal body rings, one in the layer and one in the plasma membrane. The filament ends with a capping protein, the flagellar filament is the long, helical screw that propels the bacterium when rotated by the motor, through the hook. Each protofilament is a series of protein chains. However, Campylobacter jejuni has seven protofilaments, the basal body has several traits in common with some types of secretory pores, such as the hollow, rod-like plug in their centers extending out through the plasma membrane. The bacterial flagellum is driven by an engine made up of protein

31.
Bacterial taxonomy
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Bacterial taxonomy is the taxonomy, i. e. the rank-based classification, of bacteria. In the scientific classification established by Carl von Linné, each species has to be assigned to a genus, Prokaryotes share many common features, such as lack of nuclear membrane, unicellularity, division by binary-fission and generally small size. The various species differ amongst each other based on several characteristics and he called them animalcules and published his observations in a series of letters to the Royal Society. O. F. Müller described eight species of the genus Vibrio, the term Bacterium was introduced much later, by Christian Gottfried Ehrenberg in 1838. Bacteria were first classified as plants constituting the class Schizomycetes, which along with the Schizophyceae formed the phylum Schizophyta. Haeckel in 1866 placed the group in the phylum Moneres in the kingdom Protista and defines them as completely structureless and homogeneous organisms, die Lepomoneren Protomonas—now classed as a eukaryote and not a bacterium. The name was reused in 1984 for a genus of Bacteria Vampyrella—now classed as a eukaryote. The classification of Cyanobacteria has been fought between being algae or bacteria, in 1905 Erwin F. Ferdinand Cohn recognized 4 tribes, Spherobacteria, Microbacteria, Desmobacteria, and Spirobacteria. Stanier and van Neil recognized the Kingdom Monera with 2 phyla, Myxophyta and Schizomycetae, the latter comprising classes Eubacteriae, Myxobacteriae, bisset distinguished 1 class and 4 orders, Eubacteriales, Actinomycetales, Streptomycetales, and Flexibacteriales. However, a few argue that the Archaea and Eukaryota arose from a group of bacteria. In any case, it is thought that viruses and archaea began relationships approximately two years ago, and that co-evolution may have been occurring between members of these groups. Since the Archaea and Bacteria are no more related to other than they are to eukaryotes. These lineages were formalised into the rank Domain which divided Life into 3 domains, the Eukaryota, the Archaea and this scheme is still followed today. In 1987 Carl Woese divided the Eubacteria into 11 divisions based on 16S ribosomal RNA sequences, while the three domain system is widely accepted, some authors have opposed it for various reasons. Hori and Osawas molecular analysis indicated a link between Metabacteria and eukaryotes, the only cladistic analyses for bacteria based on classical evidence largely corroborate Guptas results. He has also discovered evidence that Gram-negative bacteria arose from a symbiosis between 2 Gram-positive bacteria, classification is the grouping of organisms into progressively more inclusive groups based on phylogeny and phenotype, while nomenclature is the application of formal rules for naming organisms. The taxa which have been described are reviewed in Bergeys manual of Systematic Bacteriology. An online version of the outline of bacteria and archaea is available

32.
National Center for Biotechnology Information
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The National Center for Biotechnology Information is part of the United States National Library of Medicine, a branch of the National Institutes of Health. The NCBI is located in Bethesda, Maryland and was founded in 1988 through legislation sponsored by Senator Claude Pepper, the NCBI houses a series of databases relevant to biotechnology and biomedicine and is an important resource for bioinformatics tools and services. Major databases include GenBank for DNA sequences and PubMed, a database for the biomedical literature. Other databases include the NCBI Epigenomics database, all these databases are available online through the Entrez search engine. NCBI is directed by David Lipman, one of the authors of the BLAST sequence alignment program. He also leads a research program, including groups led by Stephen Altschul, David Landsman, Eugene Koonin, John Wilbur, Teresa Przytycka. NCBI is listed in the Registry of Research Data Repositories re3data. org, NCBI has had responsibility for making available the GenBank DNA sequence database since 1992. GenBank coordinates with individual laboratories and other databases such as those of the European Molecular Biology Laboratory. Since 1992, NCBI has grown to other databases in addition to GenBank. The NCBI assigns a unique identifier to each species of organism, the NCBI has software tools that are available by WWW browsing or by FTP. For example, BLAST is a sequence similarity searching program, BLAST can do sequence comparisons against the GenBank DNA database in less than 15 seconds. RAG2/IL2RG The NCBI Bookshelf is a collection of freely accessible, downloadable, some of the books are online versions of previously published books, while others, such as Coffee Break, are written and edited by NCBI staff. BLAST is a used for calculating sequence similarity between biological sequences such as nucleotide sequences of DNA and amino acid sequences of proteins. BLAST is a tool for finding sequences similar to the query sequence within the same organism or in different organisms. It searches the query sequence on NCBI databases and servers and post the results back to the browser in chosen format. Input sequences to the BLAST are mostly in FASTA or Genbank format while output could be delivered in variety of such as HTML, XML formatting. HTML is the output format for NCBIs web-page. Entrez is both indexing and retrieval system having data from sources for biomedical research

33.
Anammox
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Anammox, an abbreviation for ANaerobic AMMonium OXidation, is a globally important microbial process of the nitrogen cycle. The bacteria mediating this process were identified in 1999, and at the time were a surprise for the scientific community. It takes place in natural environments and anammox is also the trademarked name for the anammox-based ammonium removal technology that was developed by the Delft University of Technology. In this biological process, nitrite and ammonium ions are converted directly into diatomic nitrogen, globally, this process may be responsible for 30-50% of the N2 gas produced in the oceans. It is thus a major sink for fixed nitrogen and so limits oceanic primary productivity, the bacteria that perform the anammox process belong to the bacterial phylum Planctomycetes. Currently, five anammox genera have been discovered, Brocadia, Kuenenia, Anammoxoglobus, Jettenia, the anammox bacteria are characterized by several striking properties, they all possess one anammoxosome, a membrane bound compartment inside the cytoplasm which is the locus of anammox catabolism. Further, the membranes of these mainly consist of ladderane lipids so far unique in biology. Of special interest is the conversion to hydrazine as an intermediate, a final striking feature of the organism is the extremely slow growth rate. The doubling time is anywhere from 7–22 days, the anammox bacteria are geared towards converting their substrates at very low concentrations, in other words, they have a very high affinity to their substrates ammonium and nitrite. Anammox cells are packed with cytochrome c type proteins, including the enzymes that perform the key catabolic reactions of the anammox process, in 1932, it was reported that dinitrogen gas was generated via an unknown mechanism during fermentation in the sediments of Lake Mendota, Wisconsin, USA. More than 40 years ago, Richards noticed that most of the ammonium that should be produced during the anaerobic remineralization of organic matter was unaccounted for, as there was no known biological pathway for this transformation, biological anaerobic oxidation of ammonium received little further attention. Thirty years ago, the existence of two chemolithoautotrophic microorganisms capable of oxidizing ammonium to dinitrogen gas was predicted on the basis of thermodynamic calculations. It was thought that anaerobic oxidation of ammonium would not be feasible, by the 1990s, Arnold Mulders observations were just consistent with Richards suggestion. In their anoxic denitrifying pilot reactor, ammonium disappeared at the expense of nitrite with a clear nitrogen production, the reactor used the effluent from a methanogenic pilot reactor, which contained ammonium, sulphide and other compounds, and nitrate from a nitrifying plant as the influent. The process was named anammox, and was realized to have significance in the removal of unwanted ammonium. The discovery of the process was first publicly presented at the 5th European congress on biotechnology. By the mid-1990s, the discovery of anammox in the fluidized bed reactor was published, a maximum ammonium removal rate of 0.4 kg N/m3/d was achieved. It was shown that for every mole of ammonium consumed,0.6 mol of nitrate was required, in the same year, the biological nature of anammox was identified

34.
PubMed Identifier
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PubMed is a free search engine accessing primarily the MEDLINE database of references and abstracts on life sciences and biomedical topics. The United States National Library of Medicine at the National Institutes of Health maintains the database as part of the Entrez system of information retrieval, from 1971 to 1997, MEDLINE online access to the MEDLARS Online computerized database primarily had been through institutional facilities, such as university libraries. PubMed, first released in January 1996, ushered in the era of private, free, home-, the PubMed system was offered free to the public in June 1997, when MEDLINE searches via the Web were demonstrated, in a ceremony, by Vice President Al Gore. Information about the journals indexed in MEDLINE, and available through PubMed, is found in the NLM Catalog. As of 5 January 2017, PubMed has more than 26.8 million records going back to 1966, selectively to the year 1865, and very selectively to 1809, about 500,000 new records are added each year. As of the date,13.1 million of PubMeds records are listed with their abstracts. In 2016, NLM changed the system so that publishers will be able to directly correct typos. Simple searches on PubMed can be carried out by entering key aspects of a subject into PubMeds search window, when a journal article is indexed, numerous article parameters are extracted and stored as structured information. Such parameters are, Article Type, Secondary identifiers, Language, publication type parameter enables many special features. As these clinical girish can generate small sets of robust studies with considerable precision, since July 2005, the MEDLINE article indexing process extracts important identifiers from the article abstract and puts those in a field called Secondary Identifier. The secondary identifier field is to store numbers to various databases of molecular sequence data, gene expression or chemical compounds. For clinical trials, PubMed extracts trial IDs for the two largest trial registries, ClinicalTrials. gov and the International Standard Randomized Controlled Trial Number Register, a reference which is judged particularly relevant can be marked and related articles can be identified. If relevant, several studies can be selected and related articles to all of them can be generated using the Find related data option, the related articles are then listed in order of relatedness. To create these lists of related articles, PubMed compares words from the title and abstract of each citation, as well as the MeSH headings assigned, using a powerful word-weighted algorithm. The related articles function has been judged to be so precise that some researchers suggest it can be used instead of a full search, a strong feature of PubMed is its ability to automatically link to MeSH terms and subheadings. Examples would be, bad breath links to halitosis, heart attack to myocardial infarction, where appropriate, these MeSH terms are automatically expanded, that is, include more specific terms. Terms like nursing are automatically linked to Nursing or Nursing and this important feature makes PubMed searches automatically more sensitive and avoids false-negative hits by compensating for the diversity of medical terminology. The My NCBI area can be accessed from any computer with web-access, an earlier version of My NCBI was called PubMed Cubby

35.
Prokaryote
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A prokaryote is a unicellular organism that lacks a membrane-bound nucleus, mitochondria, or any other membrane-bound organelle. The word prokaryote comes from the Greek πρό before and καρυόν nut or kernel, prokaryotes can be divided into two domains, Archaea and bacteria. In contrast, species with nuclei and organelles are placed in the domain Eukaryota, in the prokaryotes, all the intracellular water-soluble components are located together in the cytoplasm enclosed by the cell membrane, rather than in separate cellular compartments. Bacteria, however, do possess protein-based bacterial microcompartments, which are thought to act as primitive organelles enclosed in protein shells, some prokaryotes, such as cyanobacteria may form large colonies. Others, such as myxobacteria, have multicellular stages in their life cycles, molecular studies have provided insight into the evolution and interrelationships of the three domains of biological species. Eukaryotes are organisms, including humans, whose cells have a well defined membrane-bound nucleus, the division between prokaryotes and eukaryotes reflects the existence of two very different levels of cellular organization. Distinctive types of prokaryotes include extremophiles and methanogens, these are common in extreme environments. Prokaryotes have a cytoskeleton, albeit more primitive than that of the eukaryotes. At least some also contain intracellular structures that can be seen as primitive organelles. Membranous organelles are known in some groups of prokaryotes, such as vacuoles or membrane systems devoted to special metabolic properties, in addition, some species also contain carbohydrate-enclosed microcompartments, which have distinct physiological roles. Most prokaryotes are between 1 µm and 10 µm, but they can vary in size from 0.2 µm to 750 µm, Bacteria and archaea reproduce through asexual reproduction, usually by binary fission. DNA transfer between prokaryotic cells occurs in bacteria and archaea, although it has mainly studied in bacteria. In bacteria, gene transfer occurs by three processes and these are bacterial virus -mediated transduction, plasmid-mediated conjugation, and natural transformation. Transduction of bacterial genes by bacteriophage appears to reflect an occasional error during intracellular assembly of virus particles, the transfer of bacterial DNA is under the control of the bacteriophage’s genes rather than bacterial genes. Conjugation in the well-studied E. coli system is controlled by plasmid genes, infrequently during this process, a plasmid may integrate into the host bacterial chromosome, and subsequently transfer part of the host bacterial DNA to another bacterium. Plasmid mediated transfer of host bacterial DNA also appears to be a process rather than a bacterial adaptation. Natural bacterial transformation involves the transfer of DNA from one bacterium to another through the intervening medium, for a bacterium to bind, take up and recombine donor DNA into its own chromosome, it must first enter a special physiological state called competence. About 40 genes are required in Bacillus subtilis for the development of competence, the length of DNA transferred during B. subtilis transformation can be as much as a third to the whole chromosome

Longitudinal section through the flagella area in Chlamydomonas reinhardtii. In the cell apex is the basal body that is the anchoring site for a flagellum. Basal bodies originate from and have a substructure similar to that of centrioles, with nine peripheral microtubule triplets (see structure at bottom center of image).

Conserved signature inserts and deletions (CSIs) in protein sequences provide an important category of molecular …

Figure 1: Example of a group specific Conserved signature indel (CSIs), that is specific for species from taxon X. The dashes in the alignments indicate the presence of an amino acid identical to that on the top line.

Figure 2: Multi group or Main-Line Conserved signature indel (CSI). The dashes in indicate the presence of an amino acid identical to that on the top line.

Figure 3: A concatenated protein tree showing the phylogenetic relationship of the group Thermotogae. The number of CSIs that support the branching order are indicated .

Figure 4: A concatenated protein tree showing the phylogenetic relationship of two phyla of Archaea. The number of CSIs that support the branching order are indicated .